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A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Molecular Medicine".

Deadline for manuscript submissions: closed (31 July 2024) | Viewed by 18369

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Dr. Golder N. Wilson

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1. Department of Pediatrics, Texas Tech University Health Sciences Center, Lubbock, TX, USA
2. KinderGenome Genetics Private Practice, 5347 W Mockingbird, Dallas, TX 75209, USA
Interests: genomics; syndromology; connective tissue dysplasias; Ehlers–Danlos syndrome
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Dear Colleagues,

The ability of NextGen or massive parallel sequencing technology to screen all genes in the human genome for mutations is changing the reductive one disease–one responsible gene paradigm to one of multifactorial (polygenic–environmental) causation. The multiple DNA changes defined by all-gene screening are particularly applicable to common diseases like intellectual disability (autism), diabetes, cardiomyopathy/arrhythmias, connective tissue dysplasias, and many cancers where changes in gene networks lead to spectra of disease. A combined genomic analysis of microarray and whole exome sequencing can define the respective duplication/deficiency of chromosome regions (copy number variants) and of gene sequence alterations (DNA sequence variants), the former being common in patients with intellectual disability (autism), and the latter being common in diseases affecting older children and adults. This Special Issue will begin with a brief introduction of genomics and an article contrasting its results when applied to patients with increased joint laxity (hypermobility). Patients with developmental disability and joint laxity from hypotonia of surrounding muscles will have a mixture of copy number and sequence variants, and those with laxity from dysplastic connective tissue in Ehlers–Danlos syndrome will have sequence variants in a different but overlapping network of genes. Accompanying articles that describe DNA results from genomic analysis of other common conditions ranging from cardiovascular diseases to cancer will be explored as well.

Dr. Golder N. Wilson
Guest Editor

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Keywords

genomic analysis
microarray analysis
whole exome sequencing
pathogenic mutations
copy number variants
DNA sequence variation
intellectual disability
autism
connective tissue dysplasia

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Published Papers (11 papers)

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Research

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13 pages, 2294 KiB

Open AccessArticle

Comparative Analysis of Digital Transcriptomics Between Pre- and Post-Treatment Samples of Patients with Locally Advanced Cervical Cancer: A Preliminary Study

by Sunhwa Baek, Fabian Dominik Mairinger, Sabrina Borchert, Yue Zhao, Dominik Ratiu, Peter Konrad Mallmann, Henryk Pilch and Ka-Won Noh

Curr. Issues Mol. Biol. 2024, 46(11), 12075-12087; https://doi.org/10.3390/cimb46110716 - 28 Oct 2024

Viewed by 561

Abstract

Cervical cancer remains a leading cause of cancer-related deaths in women worldwide, with limited treatment options for advanced stages and therapy-resistant cases. Despite advances in treatment, the variability in the patient response to standard therapies underscores the need for molecular biomarkers to guide personalized treatment strategies. This study aimed to explore the transcriptomic changes associated with the therapeutic response in locally advanced cervical cancer, focusing on 770 immune-related genes. We employed a digital multiplexed gene expression analysis, comparing gene expression profiles between matching pre- and post-treatment samples. The results revealed the significant upregulation of C7 and EGR2 in the post-treatment samples, suggesting that enhanced immune activity is a key factor in therapeutic success. Conversely, IL17RB, S100A7, and SAA1 were upregulated in the pre-treatment samples, potentially indicating resistance mechanisms. Pathway enrichment analysis highlighted that the immune response and apoptosis pathways are crucial to post-treatment changes. These findings suggest that C7, EGR2, and IL17RB may serve as biomarkers for predicting therapeutic outcomes and could inform the development of more effective, individualized treatment strategies for cervical cancer. This study provides new insights into the molecular mechanisms underlying treatment response and resistance. Full article

(This article belongs to the Special Issue Genomic Analysis of Common Disease)

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18 pages, 1529 KiB

Open AccessArticle

Genetics of 21-OH Deficiency and Genotype–Phenotype Correlation: Experience of the Hellenic National Referral Center

by Irene Fylaktou, Anny Mertzanian, Ioanna Farakla, Alexandros Gryparis, Ioannis Anargyros Vasilakis, Maria Binou, Evangelia Charmandari, Christina Kanaka-Gantenbein and Amalia Sertedaki

Curr. Issues Mol. Biol. 2024, 46(10), 10696-10713; https://doi.org/10.3390/cimb46100635 - 24 Sep 2024

Viewed by 580

Abstract

21-hydroxylase deficiency (21-OHD) represents the most common form of congenital adrenal hyperplasia (CAH) due to CYP21A2 gene pathogenic variants. Τhe aim of this study was the identification of CYP21A2 variants in 500 subjects of Greek origin with a suspicion of 21-OHD and, by using the existing hormonal assessment and genotypes of the 500 subjects tested, to identify a biomarker that could differentiate between the heterozygotes and the cases with no pathogenic variants identified. Five hundred subjects with clinical suspicion of 21-OHD underwent CYP21A2 gene sequencing and Multiplex Ligation Dependent Probe Amplification (MLPA). Genetic diagnosis was achieved in 27.4% of the subjects tested, most of which presented with the non-classic form (NC) of 21-OHD. Heterozygotes accounted for 42.6% of cases, whereas no pathogenic variants were identified in 27% of cases. De novo aberrations, duplications, and five novel variants were also identified. Statistical analysis revealed that the difference between the basal and 60′ post-ACTH stimulation 17-hydroxyprogesterone concentrations (Δ17-OHP^60-0) could be a potential biomarker (p < 0.05) distinguishing the heterozygotes from the cases with no pathogenic variants identified, although no clear cut-off value could be set. Further analysis revealed overlapping clinical manifestations among all the subjects tested. The presented phenotypic traits of the subjects tested and the inability to identify a discriminative biochemical marker highlight the importance of comprehensive CYP21A2 genotyping to ascertain the correct genetic diagnosis and proper genetic counselling. Full article

(This article belongs to the Special Issue Genomic Analysis of Common Disease)

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24 pages, 3305 KiB

Open AccessArticle

Clinical-Genomic Analysis of 1261 Patients with Ehlers–Danlos Syndrome Outlines an Articulo-Autonomic Gene Network (Entome)

by Golder N. Wilson and Vijay S. Tonk

Curr. Issues Mol. Biol. 2024, 46(3), 2620-2643; https://doi.org/10.3390/cimb46030166 - 19 Mar 2024

Viewed by 5100

Abstract

Systematic evaluation of 80 history and 40 history findings diagnosed 1261 patients with Ehlers–Danlos syndrome (EDS) by direct or online interaction, and 60 key findings were selected for their relation to clinical mechanisms and/or management. Genomic testing results in 566 of these patients supported EDS relevance by their differences from those in 82 developmental disability patients and by their association with general rather than type-specific EDS findings. The 437 nuclear and 79 mitochondrial DNA changes included 71 impacting joint matrix (49 COL5), 39 bone (30 COL1/2/9/11), 22 vessel (12 COL3/8VWF), 43 vessel–heart (17FBN1/11TGFB/BR), 59 muscle (28 COL6/12), 56 neural (16 SCN9A/10A/11A), and 74 autonomic (13 POLG/25porphyria related). These genes were distributed over all chromosomes but the Y, a network analogized to an ‘entome’ where DNA change disrupts truncal mechanisms (skin constraint, neuromuscular support, joint vessel flexibility) and produces a mirroring cascade of articular and autonomic symptoms. The implied sequences of genes from nodal proteins to hypermobility to branching tissue laxity or dysautonomia symptoms would be ideal for large language/artificial intelligence analyses. Full article

(This article belongs to the Special Issue Genomic Analysis of Common Disease)

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16 pages, 2657 KiB

Open AccessArticle

Exploring the Functional Basis of Epigenetic Aging in Relation to Body Fat Phenotypes in the Norfolk Island Cohort

by Thao Van Cao, Heidi G. Sutherland, Miles C. Benton, Larisa M. Haupt, Rodney A. Lea and Lyn R. Griffiths

Curr. Issues Mol. Biol. 2023, 45(10), 7862-7877; https://doi.org/10.3390/cimb45100497 - 27 Sep 2023

Viewed by 1207

Abstract

DNA methylation is an epigenetic factor that is modifiable and can change over a lifespan. While many studies have identified methylation sites (CpGs) related to aging, the relationship of these to gene function and age-related disease phenotypes remains unclear. This research explores this question by testing for the conjoint association of age-related CpGs with gene expression and the relation of these to body fat phenotypes. The study included blood-based gene transcripts and intragenic CpG methylation data from Illumina 450 K arrays in 74 healthy adults from the Norfolk Island population. First, a series of regression analyses were performed to detect associations between gene transcript level and intragenic CpGs and their conjoint relationship with age. Second, we explored how these age-related expression CpGs (eCpGs) correlated with obesity-related phenotypes, including body fat percentage, body mass index, and waist-to-hip ratio. We identified 35 age-related eCpGs associated with age. Of these, ten eCpGs were associated with at least one body fat phenotype. Collagen Type XI Alpha 2 Chain (COL11A2), Complement C1s (C1s), and four and a half LIM domains 2 (FHL2) genes were among the most significant genes with multiple eCpGs associated with both age and multiple body fat phenotypes. The COL11A2 gene contributes to the correct assembly of the extracellular matrix in maintaining the healthy structural arrangement of various components, with the C1s gene part of complement systems functioning in inflammation. Moreover, FHL2 expression was upregulated under hypermethylation in both blood and adipose tissue with aging. These results suggest new targets for future studies and require further validation to confirm the specific function of these genes on body fat regulation. Full article

(This article belongs to the Special Issue Genomic Analysis of Common Disease)

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Review

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29 pages, 1373 KiB

Open AccessReview

Unlocking the Genetic Secrets of Acromegaly: Exploring the Role of Genetics in a Rare Disorder

by Ioana Balinisteanu, Lavinia Caba, Andreea Florea, Roxana Popescu, Laura Florea, Maria-Christina Ungureanu, Letitia Leustean, Eusebiu Vlad Gorduza and Cristina Preda

Curr. Issues Mol. Biol. 2024, 46(8), 9093-9121; https://doi.org/10.3390/cimb46080538 - 20 Aug 2024

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Abstract

Acromegaly is a rare endocrine disorder characterized by the excessive production of growth hormone (GH) in adulthood. Currently, it is understood that certain pituitary neuroendocrine tumors (PitNETs) exhibit a hereditary predisposition. These tumors’ genetic patterns fall into two categories: isolated and syndromic tumors. The isolated forms are characterized by molecular defects that predispose exclusively to PitNETs, including familial isolated pituitary adenomas (FIPAs) and sporadic genetic defects not characterized by hereditary predisposition. All the categories involve either germline or somatic mutations, or both, each associated with varying levels of penetrance and different phenotypes. This highlights the importance of genetic testing and the need for a more comprehensive view of the whole disease. Despite the availability of multiple treatment options, diagnosis often occurs after several years, and management is still difficult. Early detection and intervention are crucial for preventing complications and enhancing the quality of life for affected individuals. This review aims to elucidate the molecular, clinical, and histological characteristics of GH-secreting PitNETs, providing insights into their prevalence, treatment nuances, and the benefits of genetic testing for each type of genetic disorder associated with acromegaly. Full article

(This article belongs to the Special Issue Genomic Analysis of Common Disease)

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14 pages, 1200 KiB

Open AccessReview

Genetic and Non-Genetic Contributions to Eosinophilic Granulomatosis with Polyangiitis: Current Knowledge and Future Perspectives

by Mirko Treccani, Laura Veschetti, Cristina Patuzzo, Giovanni Malerba, Augusto Vaglio and Davide Martorana

Curr. Issues Mol. Biol. 2024, 46(7), 7516-7529; https://doi.org/10.3390/cimb46070446 - 16 Jul 2024

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Abstract

In this work, we present a comprehensive overview of the genetic and non-genetic complexity of eosinophilic granulomatosis with polyangiitis (EGPA). EGPA is a rare complex systemic disease that occurs in people presenting with severe asthma and high eosinophilia. After briefly introducing EGPA and its relationship with the anti-neutrophil cytoplasmic autoantibodies (ANCA)-associated vasculitis (AAVs), we delve into the complexity of this disease. At first, the two main biological actors, ANCA and eosinophils, are presented. Biological and clinical phenotypes related to ANCA positivity or negativity are explained, as well as the role of eosinophils and their pathological subtypes, pointing out their intricate relations with EGPA. Then, the genetics of EGPA are described, providing an overview of the research effort to unravel them. Candidate gene studies have investigated biologically relevant candidate genes; the more recent genome-wide association studies and meta-analyses, able to analyze the whole genome, have confirmed previous associations and discovered novel risk loci; in the end, family-based studies have dissected the contribution of rare variants and the heritability of EGPA. Then, we briefly present the environmental contribution to EGPA, reporting seasonal events and pollutants as triggering factors. In the end, the latest omic research is discussed and the most recent epigenomic, transcriptomic and microbiome studies are presented, highlighting the current challenges, open questions and suggesting approaches to unraveling this complex disease. Full article

(This article belongs to the Special Issue Genomic Analysis of Common Disease)

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33 pages, 2088 KiB

Open AccessReview

Translation of Epigenetics in Cell-Free DNA Liquid Biopsy Technology and Precision Oncology

by Wan Ying Tan, Snigdha Nagabhyrava, Olivia Ang-Olson, Paromita Das, Luisa Ladel, Bethsebie Sailo, Linda He, Anup Sharma and Nita Ahuja

Curr. Issues Mol. Biol. 2024, 46(7), 6533-6565; https://doi.org/10.3390/cimb46070390 - 27 Jun 2024

Cited by 1 | Viewed by 2218

Abstract

Technological advancements in cell-free DNA (cfDNA) liquid biopsy have triggered exponential growth in numerous clinical applications. While cfDNA-based liquid biopsy has made significant strides in personalizing cancer treatment, the exploration and translation of epigenetics in liquid biopsy to clinical practice is still nascent. This comprehensive review seeks to provide a broad yet in-depth narrative of the present status of epigenetics in cfDNA liquid biopsy and its associated challenges. It highlights the potential of epigenetics in cfDNA liquid biopsy technologies with the hopes of enhancing its clinical translation. The momentum of cfDNA liquid biopsy technologies in recent years has propelled epigenetics to the forefront of molecular biology. We have only begun to reveal the true potential of epigenetics in both our understanding of disease and leveraging epigenetics in the diagnostic and therapeutic domains. Recent clinical applications of epigenetics-based cfDNA liquid biopsy revolve around DNA methylation in screening and early cancer detection, leading to the development of multi-cancer early detection tests and the capability to pinpoint tissues of origin. The clinical application of epigenetics in cfDNA liquid biopsy in minimal residual disease, monitoring, and surveillance are at their initial stages. A notable advancement in fragmentation patterns analysis has created a new avenue for epigenetic biomarkers. However, the widespread application of cfDNA liquid biopsy has many challenges, including biomarker sensitivity, specificity, logistics including infrastructure and personnel, data processing, handling, results interpretation, accessibility, and cost effectiveness. Exploring and translating epigenetics in cfDNA liquid biopsy technology can transform our understanding and perception of cancer prevention and management. cfDNA liquid biopsy has great potential in precision oncology to revolutionize conventional ways of early cancer detection, monitoring residual disease, treatment response, surveillance, and drug development. Adapting the implementation of liquid biopsy workflow to the local policy worldwide and developing point-of-care testing holds great potential to overcome global cancer disparity and improve cancer outcomes. Full article

(This article belongs to the Special Issue Genomic Analysis of Common Disease)

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14 pages, 899 KiB

Open AccessReview

Genetics and Epigenetics in Acquired Hemophilia A: From Bench to Bedside

by Nikolaos Evangelidis, Nikolaos Kotsiou, Paschalis Evangelidis, Vlasios I. Alevizopoulos, Iasonas Dermitzakis, Sofia Chissan, Sofia Vakalopoulou and Eleni Gavriilaki

Curr. Issues Mol. Biol. 2024, 46(6), 5147-5160; https://doi.org/10.3390/cimb46060309 - 23 May 2024

Viewed by 1460

Abstract

Acquired hemophilia A (AHA) is a bleeding disorder characterized by the immunological inhibition of factor VIII (FVIII) of the hemostatic pathway leading to hemorrhagic events. Different domains of FVIII are the target of autoantibodies (mainly immunoglobulin (Ig) G) leading to the deficiency of FVIII. Several factors have been associated with the activation of the auto-immunity towards FVIII. Emerging evidence implicates CD4+ T cell activation in mediating this autoimmune response, with their involvement like that observed in congenital hemophilia A. Several genes such as HLA II DRB*16, DQB1*0502, and CTLA-4 + 49 are responsible for the pathogenesis of AHA. Epigenetic modifications and mainly long-coding RNAS (lncRNAs) are potentially contributing to the pathogenesis of AHA. The treatment approach of AHA includes the management of acute bleeding events and the administration of immunosuppressive medications. This review aimed to summarize the published data on the genetics and epigenetics of AHA. The severity and the mortality of this disease are creating an emerging need for further research in the field of the genetics and epigenetics of acquired hemorrhagic disorder. Full article

(This article belongs to the Special Issue Genomic Analysis of Common Disease)

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11 pages, 1782 KiB

Open AccessReview

Effect of Carcinomas on Autosomal Trait Screening: A Review Article

by Husein Alhatim, Muhammad Nazrul Hakim Abdullah, Suhaili Abu Bakar and Sayed Amin Amer

Curr. Issues Mol. Biol. 2023, 45(9), 7275-7285; https://doi.org/10.3390/cimb45090460 - 4 Sep 2023

Viewed by 1790

Abstract

This review highlights the effect of carcinomas on the results of the examination of autosomal genetic traits for identification and paternity tests when carcinoid tissue is the only source and no other samples are available. In DNA typing or genetic fingerprinting, variable elements are isolated and identified within the base pair sequences that form the DNA. The person’s probable identity can be determined by analysing nucleotide sequences in particular regions of DNA unique to everyone. Genetics plays an increasingly important role in the risk stratification and management of carcinoma patients. The available information from previous studies has indicated that in some incidents, including mass disasters and crimes such as terrorist incidents, biological evidence may not be available at the scene of the accident, except for some unknown human remains found in the form of undefined human tissues. If these tissues have cancerous tumours, it may affect the examination of the genetic traits derived from these samples, thereby resulting in a failure to identify the person. Pathology units, more often, verify the identity of the patients who were diagnosed with cancer in reference to their deceased tumorous relatives. Genetic fingerprinting (GF) is also used in paternity testing when the alleged parent disappeared or died and earlier was diagnosed and treated for cancer. Full article

(This article belongs to the Special Issue Genomic Analysis of Common Disease)

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7 pages, 244 KiB

Open AccessBrief Report

Are COVID-19 Polymorphisms in ACE and ACE2 Prognosis Predictors?

by Fabiana Amaral Guarienti, Fernando Antônio Costa Xavier, Mateus Duarte Ferraz, Fernanda Wagner, Daniel Rodrigo Marinowic, Jaderson Costa da Costa and Denise Cantarelli Machado

Curr. Issues Mol. Biol. 2024, 46(8), 8111-8117; https://doi.org/10.3390/cimb46080480 - 28 Jul 2024

Viewed by 860

Abstract

Regardless of the containment of the SARS-CoV-2 pandemic, it remains paramount to comprehensively understand its underlying mechanisms to mitigate potential future health and economic impacts, comparable to those experienced throughout the course of the pandemic. The angiotensin-converting enzyme 2 (ACE2) provides anchorage for SARS-CoV-2 binding, thus implicating that ACE and ACE2 might contribute to the variability in infection severity. This study aimed to elucidate predisposing factors influencing the disease course among people infected by SARS-CoV-2, focusing on angiotensin-converting enzyme (ACE) and ACE2 polymorphisms. Notably, despite similar demographics and comorbidities, COVID-19 patients exhibit substantial differences in prognosis. Genetic polymorphisms in ACE and ACE2 have been implicated in disease progression, prompting our investigation into their role in COVID-19 evolution. Using next-generation sequencing (NGS), we analyzed ACE and ACE2 genes in a sample group comprising six subjects infected by SARS-CoV-2. Our findings revealed a correlation between specific polymorphisms and COVID-19 outcomes. Specifically, ACE and ACE2 intronic deletions were observed in all deceased patients, suggesting a potential association with mortality. These results highlight the significance of genetic factors in shaping the clinical course of COVID-19, emphasizing the importance of further research into the impact of genetic variations on COVID-19 severity. Full article

(This article belongs to the Special Issue Genomic Analysis of Common Disease)

10 pages, 894 KiB

Open AccessCase Report

Frequency of Deleterious Germline Variants in HER2-Low Breast Cancer Patients Using a Hereditary Multipanel Gene Testing

by Janaina Pontes Batista Cassoli, Ítalo Fernandes, Leonardo Carvalho, Milena Fernandes, Ana Fernanda Centrone, Letícia Taniwaki, Rita de Cássia Lima, Uelson Donizeti Rocioli Junior, Igor Wanderley Reis Dias, Patrícia Taranto, Juliana Beal, Fernanda Teresa de Lima, Fernando Moura, Miguel Cendoroglo, Sergio Eduardo Alonso Araújo and Pedro Luiz Serrano Uson Junior

Curr. Issues Mol. Biol. 2024, 46(8), 7976-7985; https://doi.org/10.3390/cimb46080471 - 25 Jul 2024

Viewed by 921

Abstract

HER2-Low is defined as low levels of HER2 expression, based on a score of 1+ on immunohistochemical (IHC) assay or as an IHC score of 2+ and negative results on in situ hybridization (ISH or FISH). They are a heterogeneous population of breast cancers that vary in prognosis and sensitivity to systemic treatments. The frequency and clinical characteristics of pathogenic germline variants (PGVs) in HER2-Low breast cancer (BC) patients is not defined. We analyzed results from patients with BC who underwent multi-gene panel testing (MGPT) (maximum 145 genes) between 2018–2019. We reclassified HER-2 status accordingly. Relationships between the variables of interest were assessed by adopting the proportional regression Cox models. Of a total of 167 BC patients who underwent MGPT, half were hormone-receptor-positive. The median age was 45 years. About two thirds of the patients were in the earlier stage of BC. A total of 57% of the cases were reclassified as HER-2-negative or -Low. PGVs were found in 19% of the patients overall, as follows: seven BRCA1, four BRCA2, two ATM, one ATR, two CFTR, three CHEK2, one FANCA, one MERTK, one MLH1, three MUTYH, one RAD50, three RAD51C, one RECQL4, and two TP53 mutations. In HER2-Low, 26.5% of the patients had PGVs, and in the overall cohort, this was 19.8%. In conclusion, differences in the prevalence of deleterious germline mutations in HER2-Low BC patients compared to non-HER2-Low BC patients were identified. Similar alterations in BRCA were observed in this group of patients compared to the overall cohort. Germline genetic tests should be evaluated in larger cohorts of patients with HER2-Low status to better address the findings. Full article

(This article belongs to the Special Issue Genomic Analysis of Common Disease)

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